AMBER Archive (2004)

Subject: AMBER: Parameters for new residue?

From: Satpal Virdee (
Date: Sat Nov 13 2004 - 13:34:27 CST

Hi all,
I'm having extreme difficulty in finding out where to start with
defining parameters for a new residue. What I have is a protein
structure in pdb format. What I want to simulate is the protein with a
cysteine covalently bonded to a pentafluorophenyl-sulfonate moiety i.e
instead of -CH2SH I have -CH2SCH2S(O2)OC6H5. This new functionality
resides within the binding site of the protein and I also want to
simulate the protein with the sulfonate group of the modified cyteine
covalently bound to an Asn of the natural substrate instead of the
pentafluorophenyl group. In both cases the new functionality is bound to
the bulk protein structure which is too large (I think for a program
such as Antechamber). Can someone point me in the right direction so
that I can read one of these strictures into Leap without getting errors
regarding the new atoms?
Thanks in advance,

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